1
|
Hu C, Zhang N, Hong Y, Tie R, Fan D, Lin A, Chen Y, Xiang LX, Shao JZ. Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity. eLife 2024; 13:RP92424. [PMID: 38497789 PMCID: PMC10948150 DOI: 10.7554/elife.92424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of the kidney in fish immune systems remains to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cells types from zebrafish kidneys via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in the kidney, suggesting the kidney acts as a secondary lymphoid organ. These results indicated that the fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune systems, and highlighted the multifaced biology of kidneys in ancient vertebrates.
Collapse
Affiliation(s)
- Chongbin Hu
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Nan Zhang
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Yun Hong
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Dongdong Fan
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Aifu Lin
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Ye Chen
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthHangzhouChina
| | - Li-xin Xiang
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
| | - Jian-zhong Shao
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang UniversityHangzhouChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| |
Collapse
|
2
|
Morabito G, Ryabova A, Valenzano DR. Immune aging in annual killifish. Immun Ageing 2024; 21:18. [PMID: 38459521 PMCID: PMC10921792 DOI: 10.1186/s12979-024-00418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Turquoise killifish (Nothobranchius furzeri) evolved a naturally short lifespan of about six months and exhibit aging hallmarks that affect multiple organs. These hallmarks include protein aggregation, telomere shortening, cellular senescence, and systemic inflammation. Turquoise killifish possess the full spectrum of vertebrate-specific innate and adaptive immune system. However, during their recent evolutionary history, they lost subsets of mucosal-specific antibody isoforms that are present in other teleosts. As they age, the immune system of turquoise killifish undergoes dramatic cellular and systemic changes. These changes involve increased inflammation, reduced antibody diversity, an increased prevalence of pathogenic microbes in the intestine, and extensive DNA damage in immune progenitor cell clusters. Collectively, the wide array of age-related changes occurring in turquoise killifish suggest that, despite an evolutionary separation spanning hundreds of millions of years, teleosts and mammals share common features of immune system aging. Hence, the spontaneous aging observed in the killifish immune system offers an excellent opportunity for discovering fundamental and conserved aspects associated with immune system aging across vertebrates. Additionally, the species' naturally short lifespan of only a few months, along with its experimental accessibility, offers a robust platform for testing interventions to improve age-related dysfunctions in the whole organism and potentially inform the development of immune-based therapies for human aging-related diseases.
Collapse
Affiliation(s)
| | - Alina Ryabova
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Dario Riccardo Valenzano
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
- Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| |
Collapse
|
3
|
Stosik M, Tokarz-Deptuła B, Deptuła W. Immunity of the intestinal mucosa in teleost fish. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108572. [PMID: 36717066 DOI: 10.1016/j.fsi.2023.108572] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The paper presents the problem of intestinal mucosa immunity in teleost fish. The immunity of the intestinal mucosa in teleost fish depends on the elements and mechanisms with different organizational/structural and functional properties than in mammals. The organization of the elements of intestinal mucosal immunitya in these animals is associated with the presence of immune cells that fulfil the functions assigned to the induction and effector sites of mucosal immunity in mammals; they are located at various histological sites of the mucosa - in the lamina propria (LP) and in the surface epithelium. The presence of mucosa-associated lymphoid tissue (MALT) has not been demonstrated in teleost fish, and the terminology used in relation to the structure and function of the mucosa immunity components in teleost fish is inadequate. In this article, we review the knowledge of intestinal mucosal immunity in teleost fish, with great potential for knowledge and practical applications especially in the field of epidemiological safety. We discuss the organization and functional properties of the elements that determine this immunity, according to current data and taking into account the tissue definition and terminology adopted by the Society for Mucosal Immunology General Assembly (13th ICMI in Tokyo, 2007).
Collapse
Affiliation(s)
- Michał Stosik
- Institute of Biological Sciences, University of Zielona Góra, Poland
| | | | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Poland
| |
Collapse
|
4
|
Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
Collapse
Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| |
Collapse
|
5
|
Waly D, Muthupandian A, Fan CW, Anzinger H, Magor BG. Immunoglobulin VDJ repertoires reveal hallmarks of germinal centers in unique cell clusters isolated from zebrafish ( Danio rerio) lymphoid tissues. Front Immunol 2022; 13:1058877. [PMID: 36569890 PMCID: PMC9772432 DOI: 10.3389/fimmu.2022.1058877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/03/2022] [Indexed: 12/13/2022] Open
Abstract
DNA mutagenesis during antibody affinity maturation has potentially oncogenic or autoimmune outcomes if not tightly controlled as it is in mammalian germinal centers. Cold blooded vertebrates lack germinal centers, yet have a functional Ig gene mutator enzyme, Aicda. In fish there are clusters of Aicda+ cells encircled by pigmented 'melano-macrophages' and we test the hypothesis that these clusters are functionally analogous to germinal centers. Sequenced IgH VDJ repertoire libraries from individual isolated clusters showed evidence of B-cell clonal expansion and VDJ somatic hypermutation. Construction of Ig clonal lineage trees revealed that unlike surrounding lymphoid tissue, each cluster is dominated by a few B-cell VDJ clonotypes having hundreds of mutated variants. Recruitment of B-cells to the clusters appears to be ongoing, as there are additional Ig clones having smaller lineages. Finally, we show evidence for positive selection for replacement mutations in regions encoding the antigen contact loops, but not in the framework regions, consistent with functional antibody modification. Melano-macrophages appear to trap the Ag used for post-mutation B-cell selection, performing a role analogous to the follicular dendritic cells of mammalian germinal centers. These findings provide insights into the evolution of the affinity maturation process, the improvement of fish vaccines and possibly also the workings of atypical ectopic germinal centers generated in several human diseases.
Collapse
Affiliation(s)
- Doaa Waly
- *Correspondence: Brad G. Magor, ; Doaa Waly,
| | | | | | | | | |
Collapse
|
6
|
Garcia B, Dong F, Casadei E, Rességuier J, Ma J, Cain KD, Castrillo PA, Xu Z, Salinas I. A Novel Organized Nasopharynx-Associated Lymphoid Tissue in Teleosts That Expresses Molecular Markers Characteristic of Mammalian Germinal Centers. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2215-2226. [PMID: 36426979 DOI: 10.4049/jimmunol.2200396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023]
Abstract
Nasal immunity is an ancient and conserved arm of the mucosal immune system in vertebrates. In teleost fish, we previously reported the presence of a nasopharynx-associated lymphoid tissue (NALT) characterized by scattered immune cells located in the trout olfactory lamellae. This diffuse NALT mounts innate and adaptive immune responses to nasal infection or vaccination. In mammals, lymphoid structures such as adenoids and tonsils support affinity maturation of the adaptive immune response in the nasopharyngeal cavity. These structures, known as organized NALT (O-NALT), have not been identified in teleost fish to date, but their evolutionary forerunners exist in sarcopterygian fish. In this study, we report that the rainbow trout nasal cavity is lined with a lymphoepithelium that extends from the most dorsal opening of the nares to the ventral nasal cavity. Within the nasal lymphoepithelium we found lymphocyte aggregates called O-NALT in this study that are composed of ∼ 56% CD4+, 24% IgM+, 16% CD8α+, and 4% IgT+ lymphocytes and that have high constitutive aicda mRNA expression. Intranasal (i.n.) vaccination with live attenuated infectious hematopoietic necrosis virus triggers expansions of B and T cells and aicda expression in response to primary i.n. vaccination. IgM+ B cells undergo proliferation and apoptosis within O-NALT upon prime but not boost i.n. vaccination. Our results suggest that novel mucosal microenvironments such as O-NALT may be involved in the affinity maturation of the adaptive immune response in early vertebrates.
Collapse
Affiliation(s)
- Benjamin Garcia
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM
| | - Fen Dong
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM.,Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, China
| | - Elisa Casadei
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM
| | - Julien Rességuier
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jie Ma
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; and
| | - Kenneth D Cain
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID; and
| | - Pedro A Castrillo
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM.,Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Zhen Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, China
| | - Irene Salinas
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM
| |
Collapse
|
7
|
Muthupandian A, Waly D, Magor BG. Do ectothermic vertebrates have a home in which to affinity mature their antibody responses? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 119:104021. [PMID: 33482240 DOI: 10.1016/j.dci.2021.104021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
There has been a longstanding question of whether affinity maturation occurs in ectotherms, and if it does, where in tissues this happens. Although cold-blooded vertebrates (ectotherms) lack histologically discernible germinal centers, they have a fully functional Ig gene mutator enzyme (activation-induced cytidine deaminase: AID or Aicda). Protein and Ig cDNA transcript analyses provide evidence that ectotherms can, under certain conditions, demonstrate antibody affinity maturation, and somatic hypermutation of their Ig genes during secondary immune responses. Here, we review the evidence for antibody affinity maturation and somatic hypermutation of Ig V(D)J exons. We argue that past evidence of long-term intact antigen retention, and recent studies of in situ expression of AID transcripts, point to fish melanomacrophage clusters as sites functionally analogous to a germinal center. Recent work in zebrafish provides a way forward to test these predictions through V(D)J repertoire analyses on isolated, intact melanomacrophage clusters. This work has implications not only for vaccine use in aquaculture, but also for antibody affinity maturation processes in all ectothermic vertebrates.
Collapse
Affiliation(s)
- A Muthupandian
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB, T6G-2E5, Canada
| | - D Waly
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB, T6G-2E5, Canada
| | - B G Magor
- Dept. of Biological Sciences, University of Alberta, Edmonton, AB, T6G-2E5, Canada.
| |
Collapse
|
8
|
Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
Collapse
Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M. Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
9
|
Epidermal Club Cells in Fishes: A Case for Ecoimmunological Analysis. Int J Mol Sci 2021; 22:ijms22031440. [PMID: 33535506 PMCID: PMC7867084 DOI: 10.3390/ijms22031440] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
Epidermal club cells (ECCs), along with mucus cells, are present in the skin of many fishes, particularly in the well-studied Ostariophysan family Cyprinidae. Most ECC-associated literature has focused on the potential role of ECCs as a component of chemical alarm cues released passively when a predator damages the skin of its prey, alerting nearby prey to the presence of an active predator. Because this warning system is maintained by receiver-side selection (senders are eaten), there is want of a mechanism to confer fitness benefits to the individual that invests in ECCs to explain their evolutionary origin and maintenance in this speciose group of fishes. In an attempt to understand the fitness benefits that accrue from investment in ECCs, we reviewed the phylogenetic distribution of ECCs and their histochemical properties. ECCs are found in various forms in all teleost superorders and in the chondrostei inferring either early or multiple independent origins over evolutionary time. We noted that ECCs respond to several environmental stressors/immunomodulators including parasites and pathogens, are suppressed by immunomodulators such as testosterone and cortisol, and their density covaries with food ration, demonstrating a dynamic metabolic cost to maintaining these cells. ECC density varies widely among and within fish populations, suggesting that ECCs may be a convenient tool with which to assay ecoimmunological tradeoffs between immune stress and foraging activity, reproductive state, and predator-prey interactions. Here, we review the case for ECC immune function, immune functions in fishes generally, and encourage future work describing the precise role of ECCs in the immune system and life history evolution in fishes.
Collapse
|
10
|
Bilal S, Etayo A, Hordvik I. Immunoglobulins in teleosts. Immunogenetics 2021; 73:65-77. [PMID: 33439286 DOI: 10.1007/s00251-020-01195-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023]
Abstract
Immunoglobulins are glycoproteins which are produced as membrane-bound receptors on B-cells or in a secreted form, known as antibodies. In teleosts, three immunoglobulin isotypes, IgM, IgT, and IgD, are present, each comprising two identical heavy and two identical light polypeptide chains. The basic mechanisms for generation of immunoglobulin diversity are similar in teleosts and higher vertebrates. The B-cell pre-immune repertoire is diversified by VDJ recombination, junctional flexibility, addition of nucleotides, and combinatorial association of light and heavy chains, while the post-immune repertoire undergoes somatic hypermutation during clonal expansion. Typically, the teleost immunoglobulin heavy chain gene complex has a modified translocon arrangement where the Dτ-Jτ-Cτ cluster of IgT is generally located between the variable heavy chain (VH) region and the Dμ/δ-Jμ/δ-Cμ-Cδ gene segments, or within the set of VH gene segments. However, multiple genome duplication and deletion events and loss of some individual genes through evolution has complicated the IgH gene organization. The IgH gene arrangement allows the expression of either IgT or IgM/IgD. Alternative splicing is responsible for the regulation of IgM/IgD expression and the secreted versus transmembrane forms of IgT, IgD, and IgM. The overall structure of IgM and IgT is usually conserved across species, whereas IgD has a large variety of structures. IgM is the main effector molecule in both systemic and mucosal immunity and shows a broad range of concentrations in different teleost species. Although IgM is usually present in higher concentrations under normal conditions, IgT is considered the main mucosal Ig.
Collapse
Affiliation(s)
- Sumaira Bilal
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Angela Etayo
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ivar Hordvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
| |
Collapse
|
11
|
Semple SL, Dixon B. Salmonid Antibacterial Immunity: An Aquaculture Perspective. BIOLOGY 2020; 9:E331. [PMID: 33050557 PMCID: PMC7599743 DOI: 10.3390/biology9100331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023]
Abstract
The aquaculture industry is continuously threatened by infectious diseases, including those of bacterial origin. Regardless of the disease burden, aquaculture is already the main method for producing fish protein, having displaced capture fisheries. One attractive sector within this industry is the culture of salmonids, which are (a) uniquely under pressure due to overfishing and (b) the most valuable finfish per unit of weight. There are still knowledge gaps in the understanding of fish immunity, leading to vaccines that are not as effective as in terrestrial species, thus a common method to combat bacterial disease outbreaks is the use of antibiotics. Though effective, this method increases both the prevalence and risk of generating antibiotic-resistant bacteria. To facilitate vaccine design and/or alternative treatment efforts, a deeper understanding of the teleost immune system is essential. This review highlights the current state of teleost antibacterial immunity in the context of salmonid aquaculture. Additionally, the success of current techniques/methods used to combat bacterial diseases in salmonid aquaculture will be addressed. Filling the immunology knowledge gaps highlighted here will assist in reducing aquaculture losses in the future.
Collapse
Affiliation(s)
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| |
Collapse
|
12
|
Smith NC, Rise ML, Christian SL. A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish. Front Immunol 2019; 10:2292. [PMID: 31649660 PMCID: PMC6795676 DOI: 10.3389/fimmu.2019.02292] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.
Collapse
Affiliation(s)
- Nicole C Smith
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sherri L Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| |
Collapse
|
13
|
Patel B, Banerjee R, Samanta M, Das S. Diversity of Immunoglobulin (Ig) Isotypes and the Role of Activation-Induced Cytidine Deaminase (AID) in Fish. Mol Biotechnol 2018; 60:435-453. [PMID: 29704159 DOI: 10.1007/s12033-018-0081-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The disparate diversity in immunoglobulin (Ig) repertoire has been a subject of fascination since the emergence of prototypic adaptive immune system in vertebrates. The carboxy terminus region of activation-induced cytidine deaminase (AID) has been well established in tetrapod lineage and is crucial for its function in class switch recombination (CSR) event of Ig diversification. The absence of CSR in the paraphyletic group of fish is probably due to changes in catalytic domain of AID and lack of cis-elements in IgH locus. Therefore, understanding the arrangement of Ig genes in IgH locus and functional facets of fish AID opens up new realms of unravelling the alternative mechanisms of isotype switching and antibody diversity. Further, the teleost AID has been recently reported to have potential of catalyzing CSR in mammalian B cells by complementing AID deficiency in them. In that context, the present review focuses on the recent advances regarding the generation of diversity in Ig repertoire in the absence of AID-regulated class switching in teleosts and the possible role of T cell-independent pathway involving B cell activating factor and a proliferation-inducing ligand in activation of CSR machinery.
Collapse
Affiliation(s)
- Bhakti Patel
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Rajanya Banerjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Mrinal Samanta
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751 002, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India.
| |
Collapse
|
14
|
Abstract
The adaptive immune system arose 500 million years ago in ectothermic (cold-blooded) vertebrates. Classically, the adaptive immune system has been defined by the presence of lymphocytes expressing recombination-activating gene (RAG)-dependent antigen receptors and the MHC. These features are found in all jawed vertebrates, including cartilaginous and bony fish, amphibians and reptiles and are most likely also found in the oldest class of jawed vertebrates, the extinct placoderms. However, with the discovery of an adaptive immune system in jawless fish based on an entirely different set of antigen receptors - the variable lymphocyte receptors - the divergence of T and B cells, and perhaps innate-like lymphocytes, goes back to the origin of all vertebrates. This Review explores how recent developments in comparative immunology have furthered our understanding of the origins and function of the adaptive immune system.
Collapse
Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, USA.
| |
Collapse
|
15
|
Haakenson JK, Huang R, Smider VV. Diversity in the Cow Ultralong CDR H3 Antibody Repertoire. Front Immunol 2018; 9:1262. [PMID: 29915599 PMCID: PMC5994613 DOI: 10.3389/fimmu.2018.01262] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023] Open
Abstract
Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique “stalk and knob” structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
Collapse
Affiliation(s)
- Jeremy K Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruiqi Huang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| |
Collapse
|
16
|
Ito F, Yang H, Xiao X, Li SX, Wolfe A, Zirkle B, Arutiunian V, Chen XS. Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H. Sci Rep 2018; 8:3763. [PMID: 29491387 PMCID: PMC5830531 DOI: 10.1038/s41598-018-21955-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Abstract
APOBEC3H (A3H) is a member of the APOBEC3 subfamily of DNA cytosine deaminases that are important for innate immune defense and have been implicated in cancer biogenesis. To understand the structural basis for A3H biochemical function, we determined a high-resolution structure of human A3H and performed extensive biochemical analysis. The 2.49 Å crystal structure reveals a uniquely long C-terminal helix 6 (h6), a disrupted β5 strand of the canonical five-stranded β-sheet core, and a long loop 1 around the Zn-active center. Mutation of a loop 7 residue, W115, disrupted the RNA-mediated dimerization of A3H yielding an RNA-free monomeric form that still possessed nucleic acid binding and deaminase activity. A3H expressed in HEK293T cells showed RNA dependent HMW complex formation and RNase A-dependent deaminase activity. A3H has a highly positively charged surface surrounding the Zn-active center, and multiple positively charged residues within this charged surface play an important role in the RNA-mediated HMW formation and deaminase inhibition. Furthermore, these positively charged residues affect subcellular localization of A3H between the nucleus and cytosol. Finally, we have identified multiple residues of loop 1 and 7 that contribute to the overall deaminase activity and the methylcytosine selectivity.
Collapse
Affiliation(s)
- Fumiaki Ito
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Xiao Xiao
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Infectious Diseases and Vaccines Research, Merck Research Laboratories, Merck & Co., Inc, West Point, PA, USA
| | - Shu-Xing Li
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA
| | - Aaron Wolfe
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Brett Zirkle
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vagan Arutiunian
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA. .,Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA. .,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA. .,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
17
|
Dickerson HW, Findly RC. Vertebrate Adaptive Immunity-Comparative Insights from a Teleost Model. Front Immunol 2017; 8:1379. [PMID: 29123524 PMCID: PMC5662878 DOI: 10.3389/fimmu.2017.01379] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/06/2017] [Indexed: 11/13/2022] Open
Abstract
The channel catfish (Ictalurus punctatus) and the ciliated protozoan parasite Ichthyophthirius multifiliis are used to study pathogen-specific protective immunity. In this review, we briefly describe this host–parasite system and discuss the comparative insights it provides on the adaptive immune response of vertebrates. We include studies related to cutaneous mucosal immunity, B cell memory responses, and analyses of αβ T cell receptor (TCR) repertoires. This host–parasite model has played an important role in elucidating host protective responses to parasite invasion and for comparative studies of vertebrate immunity. Recent findings from bioinformatics analyses of TCR β repertoires suggest that channel catfish preferentially expand specific clonotypes that are stably integrated in the genome. This finding could have broad implications related to diversity in lymphocyte receptors of early vertebrates.
Collapse
Affiliation(s)
- Harry W Dickerson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Robert Craig Findly
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| |
Collapse
|
18
|
Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans. Mol Cell Biol 2017; 37:MCB.00077-17. [PMID: 28716949 DOI: 10.1128/mcb.00077-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/10/2017] [Indexed: 01/17/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties.
Collapse
|
19
|
Abstract
Apolipoprotein B mRNA Editing Catalytic Polypeptide-like 1 or APOBEC1 was discovered in 1993 as the zinc-dependent cytidine deaminase responsible for the production of an in frame stop codon in apoB mRNA through modification of cytidine at nucleotide position 6666 to uridine. At the time of this discovery there was much speculation concerning the mechanism of base modification RNA editing which has been rekindled by the discovery of multiple C to U RNA editing events in the 3′ UTRs of mRNAs and the finding that other members of the APOBEC family while able to bind RNA, have the biological function of being DNA mutating enzymes. Current research is addressing the mechanism for these nucleotide modification events that appear not to adhere to the mooring sequence-dependent model for APOBEC1 involving the assembly of a multi protein containing editosome. This review will summarize our current understanding of the structure and function of APOBEC proteins and examine how RNA binding to them may be a regulatory mechanism.
Collapse
Affiliation(s)
- Harold C Smith
- a University of Rochester, School of Medicine and Dentistry , Department of Biochemistry and Biophysics , Rochester , NY , USA
| |
Collapse
|
20
|
Sutherland DB, Suzuki K, Fagarasan S. Fostering of advanced mutualism with gut microbiota by Immunoglobulin A. Immunol Rev 2016; 270:20-31. [PMID: 26864102 DOI: 10.1111/imr.12384] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immunoglobulin A (IgA), the most abundantly secreted antibody isotype in mammals, not only provides direct immune protection to neonates via maternal milk but also helps program the infant immune system by regulating the microbiota. IgA continues to maintain dynamic interactions with the gut microbiota throughout life and this influences immune system homeostasis as well as other physiological processes. The secretory IgA produced independently of T-cell selection are commonly referred to as natural or innate antibodies. Our studies have shown that innate-IgA, while effective at excluding microorganisms from the gut, does not promote mutualism with the microbiota in the same way as adaptive-IgA that is selected in T cell-dependent germinal center reactions. Adaptive-IgA fosters more advanced mutualism with the microbiota than innate-IgA by selecting and diversifying beneficial microbial communities. In this review, we suggest that the diversified microbiota resulting from adaptive-IgA pressure was pivotal in promoting ecological adaptability and speciation potential of mammals.
Collapse
Affiliation(s)
- Duncan B Sutherland
- Laboratory of Intestinal Immunology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Keiichiro Suzuki
- Center for Innovation in Immunoregulative Technology and Therapeutics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sidonia Fagarasan
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Institute, Yokohama, Japan
| |
Collapse
|
21
|
Xu J, Zhao J, Li Y, Zou Y, Lu B, Chen Y, Ma Y, Xu H. Evaluation of differentially expressed immune-related genes in intestine of Pelodiscus sinensis after intragastric challenge with lipopolysaccharide based on transcriptome analysis. FISH & SHELLFISH IMMUNOLOGY 2016; 56:417-426. [PMID: 27475104 DOI: 10.1016/j.fsi.2016.07.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/01/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Pelodiscus sinensis is the most common turtle species that has been raised in East and Southeast Asia. However, there are still limited studies about the immune defense mechanisms in its small intestine until now. In the present research, histological analysis and transcriptome analysis was performed on the small intestine of P. sinensis after intragastric challenge with LPS to explore its mechanisms of immune responses to pathogens. The result showed the number of intraepithelial lymphocytes (IELs) and goblet cells (GCs) in its intestine increased significantly at 48 h post-challenge with LPS by intragastrical route, indicating clearly the intestinal immune response was induced. Compared with the control, a total of 748 differentially expressed genes (DEGs) were identified, including 361 up-regulated genes and 387 down-regulated genes. Based on the Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG), 48 immune-related DEGs were identified, which were classified into 82 GO terms and 14 pathways. Finally, 18 DEGs, which were randomly selected, were confirmed by quantitative real-time PCR (qRT-PCR). Our results provide valuable information for further analysis of the immune defense mechanisms against pathogens in the small intestine of P. sinensis.
Collapse
Affiliation(s)
- Jiehao Xu
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jing Zhao
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Yiqun Li
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Yiyi Zou
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Binjie Lu
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Yuyin Chen
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Youzhi Ma
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Haisheng Xu
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
| |
Collapse
|
22
|
Antibody Affinity Maturation in Fishes-Our Current Understanding. BIOLOGY 2015; 4:512-24. [PMID: 26264036 PMCID: PMC4588147 DOI: 10.3390/biology4030512] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/13/2015] [Accepted: 07/23/2015] [Indexed: 12/15/2022]
Abstract
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes.
Collapse
|
23
|
Abstract
As in mammals, cartilaginous and teleost fishes possess adaptive immune systems based on antigen recognition by immunoglobulins (Ig), T cell receptors (TCR), and major histocompatibility complex molecules (MHC) I and MHC II molecules. Also it is well established that fish B cells and mammalian B cells share many similarities, including Ig gene rearrangements, and production of membrane Ig and secreted Ig forms. This chapter provides an overview of the IgH and IgL chains in cartilaginous and bony fish, including their gene organizations, expression, diversity of their isotypes, and development of the primary repertoire. Furthermore, when possible, we have included summaries of key studies on immune mechanisms such as allelic exclusion, somatic hypermutation, affinity maturation, class switching, and mucosal immune responses.
Collapse
Affiliation(s)
- Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
| |
Collapse
|
24
|
Shimoda N, Hirose K, Kaneto R, Izawa T, Yokoi H, Hashimoto N, Kikuchi Y. No evidence for AID/MBD4-coupled DNA demethylation in zebrafish embryos. PLoS One 2014; 9:e114816. [PMID: 25536520 PMCID: PMC4275248 DOI: 10.1371/journal.pone.0114816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 10/28/2014] [Indexed: 12/20/2022] Open
Abstract
The mechanisms responsible for active DNA demethylation remain elusive in Metazoa. A previous study that utilized zebrafish embryos provided a potent mechanism for active demethylation in which three proteins, AID, MBD4, and GADD45 are involved. We recently found age-dependent DNA hypomethylation in zebrafish, and it prompted us to examine if AID and MBD4 could be involved in the phenomenon. Unexpectedly, however, we found that most of the findings in the previous study were not reproducible. First, the injection of a methylated DNA fragment into zebrafish eggs did not affect either the methylation of genomic DNA, injected methylated DNA itself, or several loci tested or the expression level of aid, which has been shown to play a role in demethylation. Second, aberrant methylation was not observed at certain CpG islands following the injection of antisense morpholino oligonucleotides against aid and mbd4. Furthermore, we demonstrated that zebrafish MBD4 cDNA lacked a coding region for the methyl-CpG binding domain, which was assumed to be necessary for guidance to target regions. Taken together, we concluded that there is currently no evidence to support the proposed roles of AID and MBD4 in active demethylation in zebrafish embryos.
Collapse
Affiliation(s)
- Nobuyoshi Shimoda
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 35 Gengo, Morioka, Obu, Aichi 474-8522, Japan
- * E-mail:
| | - Kentaro Hirose
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Reiya Kaneto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Toshiaki Izawa
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Hayato Yokoi
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumi-Dori Amamiya-Machi, Aoba-Ku, Sendai 981-8555, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 35 Gengo, Morioka, Obu, Aichi 474-8522, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| |
Collapse
|
25
|
Pettinello R, Dooley H. The immunoglobulins of cold-blooded vertebrates. Biomolecules 2014; 4:1045-69. [PMID: 25427250 PMCID: PMC4279169 DOI: 10.3390/biom4041045] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 12/27/2022] Open
Abstract
Although lymphocyte-like cells secreting somatically-recombining receptors have been identified in the jawless fishes (hagfish and lamprey), the cartilaginous fishes (sharks, skates, rays and chimaera) are the most phylogenetically distant group relative to mammals in which bona fide immunoglobulins (Igs) have been found. Studies of the antibodies and humoral immune responses of cartilaginous fishes and other cold-blooded vertebrates (bony fishes, amphibians and reptiles) are not only revealing information about the emergence and roles of the different Ig heavy and light chain isotypes, but also the evolution of specialised adaptive features such as isotype switching, somatic hypermutation and affinity maturation. It is becoming increasingly apparent that while the adaptive immune response in these vertebrate lineages arose a long time ago, it is most definitely not primitive and has evolved to become complex and sophisticated. This review will summarise what is currently known about the immunoglobulins of cold-blooded vertebrates and highlight the differences, and commonalities, between these and more “conventional” mammalian species.
Collapse
Affiliation(s)
- Rita Pettinello
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
| |
Collapse
|
26
|
Iwanami N. Zebrafish as a model for understanding the evolution of the vertebrate immune system and human primary immunodeficiency. Exp Hematol 2014; 42:697-706. [PMID: 24824573 DOI: 10.1016/j.exphem.2014.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/21/2014] [Accepted: 05/02/2014] [Indexed: 01/04/2023]
Abstract
Zebrafish is an important vertebrate model that provides the opportunity for the combination of genetic interrogation with advanced live imaging in the analysis of complex developmental and physiologic processes. Among the many advances that have been achieved using the zebrafish model, it has had a great impact on immunology. Here, I discuss recent work focusing on the genetic underpinnings of the development and function of lymphocytes in fish. Lymphocytes play critical roles in vertebrate-specific acquired immune systems of jawless and jawed fish. The unique opportunities afforded by the ability to carry out forward genetic screens and the rapidly evolving armamentarium of reverse genetics in fish usher in a new immunologic research that complements the traditional models of chicken and mouse. Recent work has greatly increased our understanding of the molecular components of the zebrafish immune system, identifying evolutionarily conserved and fish-specific functions of immune-related genes. Interestingly, some of the genes whose mutations underlie the phenotypes in immunodeficient zebrafish were also identified in immunodeficient human patients. In addition, because of the generally conserved structure and function of immune facilities, the zebrafish also provides a versatile model to examine the functional consequences of genetic variants in immune-relevant genes in the human population. Thus, I propose that genetic approaches using the zebrafish hold great potential for a better understanding of molecular mechanisms of human primary immunodeficiencies and the evolution of vertebrate immune systems.
Collapse
Affiliation(s)
- Norimasa Iwanami
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| |
Collapse
|
27
|
Mashoof S, Pohlenz C, Chen PL, Deiss TC, Gatlin D, Buentello A, Criscitiello MF. Expressed IgH μ and τ transcripts share diversity segment in ranched Thunnus orientalis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 43:76-86. [PMID: 24231183 PMCID: PMC7039072 DOI: 10.1016/j.dci.2013.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/07/2013] [Accepted: 10/30/2013] [Indexed: 05/23/2023]
Abstract
It is now appreciated that in addition to the immunoglobulin (Ig)M and D isotypes fish also make the mucosal IgT. In this study we sequenced the full length of Ig τ as well as μ in the commercially important Thunnus orientalis (Pacific bluefin tuna), the first molecular analysis of these two Ig isotypes in a member of the order Perciformes. Tuna IgM and IgT are each composed of four constant (CH) domains. We cloned and sequenced 48 different variable (VH) domain gene rearrangements of tuna immunoglobulins and grouped the VH gene sequences to four VH gene segment families based on 70% nucleotide identity. Three VH gene families were used by both IgM and IgT but one group was only found to be used by IgM. Most interestingly, both μ and τ clones appear to use the same diversity (DH) segment, unlike what has been described in other species, although they have dedicated IgT and IgM joining (JH) gene segments. We complemented this repertoire study with phylogenetic and tissue expression analysis. In addition to supporting the development of humoral vaccines in this important aquaculture species, these data suggest that the DH-JH recombination rather than the VH-DH recombination may be instructive for IgT versus IgM/D bearing lymphocyte lineages in some fish.
Collapse
Affiliation(s)
- Sara Mashoof
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Camilo Pohlenz
- Department of Wildlife and Fisheries Sciences, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Patricia L Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Delbert Gatlin
- Department of Wildlife and Fisheries Sciences, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Alejandro Buentello
- Schillinger Genetics, 4401 Westown Parkway Suite 225, West Des Moines, IA 50266, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
28
|
Saha NR, Ota T, Litman GW, Hansen J, Parra Z, Hsu E, Buonocore F, Canapa A, Cheng JF, Amemiya CT. Genome complexity in the coelacanth is reflected in its adaptive immune system. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:438-63. [PMID: 24464682 DOI: 10.1002/jez.b.22558] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/23/2013] [Indexed: 01/09/2023]
Abstract
We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.
Collapse
Affiliation(s)
- Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Villota-Herdoiza D, Pila EA, Quiniou S, Waldbieser GC, Magor BG. Transcriptional regulation of teleost Aicda genes. Part 1 - suppressors of promiscuous promoters. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1981-1987. [PMID: 24161771 DOI: 10.1016/j.fsi.2013.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 06/02/2023]
Abstract
In order to better understand antibody affinity maturation in fishes we sought to identify gene regulatory elements that could drive expression of activated B-cell specific fluorescent reporter transgenes in zebrafish. Specifically the promoter and several non-coding regions of the channel catfish (Ictalurus punctatus) and zebrafish (Danio rerio) were tested for transcriptional activity using a dual luciferase reporter system in transfected fish leukocytes and two mammalian cell lines that constitutively express Aicda (activation-induced cytidine deaminase). The promoters of both fish Aicda genes were as transcriptionally active as an SV40 promoter control in all cell lines tested, regardless of the cells ability to express Aicda. Coupling of a putative intron 1 enhancer or a region 10 kb upstream of the zebrafish promoter effectively silenced transcription from the fish Aicda promoter. Paradoxically these suppressor elements enhanced transcription when they were coupled to the mouse Aicda intron 1 enhancer. The results are considered in context of similar observations for Aicda transcriptional regulation in mice and in light of recent evidence that Aicda is utilized for epigenetic reprogramming of several non-lymphoid cell types.
Collapse
Affiliation(s)
- Daniela Villota-Herdoiza
- Dept. of Biological Sciences, University of Alberta, CW405 BioSci Bldg., Edmonton, AB T6G-2E5, Canada.
| | | | | | | | | |
Collapse
|
30
|
Chowdhury S, Kitamura K, Simadu M, Koura M, Muramatsu M. Concerted action of activation-induced cytidine deaminase and uracil-DNA glycosylase reduces covalently closed circular DNA of duck hepatitis B virus. FEBS Lett 2013; 587:3148-52. [PMID: 23954625 DOI: 10.1016/j.febslet.2013.07.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/24/2013] [Indexed: 12/29/2022]
Abstract
Covalently closed circular DNA (cccDNA) forms a template for the replication of hepatitis B virus (HBV) and duck HBV (DHBV). Recent studies suggest that activation-induced cytidine deaminase (AID) functions in innate immunity, although its molecular mechanism of action remains unclear, particularly regarding HBV restriction. Here we demonstrated that overexpression of chicken AID caused hypermutation and reduction of DHBV cccDNA levels. Inhibition of uracil-DNA glycosylase (UNG) by UNG inhibitor protein (UGI) abolished AID-induced cccDNA reduction, suggesting that the AID/UNG pathway triggers the degradation of cccDNA via cytosine deamination and uracil excision.
Collapse
Affiliation(s)
- Sajeda Chowdhury
- Department of Molecular Genetics, Kanazawa University, Graduate School of Medical Sciences, Kanazawa, Japan
| | | | | | | | | |
Collapse
|
31
|
Capolunghi F, Rosado MM, Sinibaldi M, Aranburu A, Carsetti R. Why do we need IgM memory B cells? Immunol Lett 2013; 152:114-20. [PMID: 23660557 DOI: 10.1016/j.imlet.2013.04.007] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 12/22/2022]
Abstract
Immunological memory is our reservoir of ready-to-use antibodies and memory B cells. Because of immunological memory a secondary infection will be very light or not occur at all. Antibodies and cells, generated in the germinal center in response to the first encounter with antigen, are highly specific, remain in the organism virtually forever and are mostly of IgG isotype. Long lived plasma cells homing to the bone marrow ensure the constant production of protective antibodies, whereas switched memory B cells proliferate and differentiate in response to secondary challenge. IgM memory B cells represent our first-line defense against infections. They are generated by a T-cell independent mechanism probably triggered by Toll-like receptor-9. They produce natural antibodies with anti-bacterial specificity and the spleen is indispensable for their maintenance. We will review the characteristics and functions of IgM memory B cells that explain their importance in the immediate protection from pathogens. IgM memory B cells, similar to mouse B-1a B cells, may be a remnant of a primitive immune system that developed in the spleen of cartilaginous fish and persisted throughout evolution notwithstanding the sophisticated tools of the adaptive immune system.
Collapse
Affiliation(s)
- Federica Capolunghi
- Department of Laboratories, Children Hospital Bambino Gesù (IRCCS), Piazza S.Onofrio 4, 00165 Rome, Italy
| | | | | | | | | |
Collapse
|
32
|
Vuong BQ, Chaudhuri J. Combinatorial mechanisms regulating AID-dependent DNA deamination: interacting proteins and post-translational modifications. Semin Immunol 2012; 24:264-72. [PMID: 22771392 DOI: 10.1016/j.smim.2012.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
Abstract
Protective humoral immune responses result from immunoglobulin (Ig) diversification reactions that proceed through programmed DNA double-strand breaks and mutations in developing or mature B cells. While primary Ig diversity is dependent on V(D)J recombination and the RAG proteins, secondary diversification is achieved through class switch recombination (CSR) and somatic hypermutation (SHM), which require AID (activation induced deaminase). Because aberrant AID activity can result in mutations in non-Ig loci and DNA translocations between the Ig locus and non-Ig genes, the activity of AID must be stringently regulated. AID mRNA expression is regulated transcriptionally by cytokine stimulation and post-transcriptionally by miRNAs. AID activity is regulated by post-translational modifications, subcellular localization, and interaction with other proteins. All of these molecular mechanisms have evolved to specifically induce AID-dependent mutations and DNA double-strand breaks at the Ig loci to promote maximal Ig gene diversification while limiting the access of this mutator to non-Ig regions.
Collapse
Affiliation(s)
- Bao Q Vuong
- Immunology Program, Memorial Sloan-Kettering Cancer Center, Gerstner Sloan-Kettering Graduate School, 1275 York Avenue, New York, NY 10065, United States.
| | | |
Collapse
|
33
|
Kato L, Stanlie A, Begum NA, Kobayashi M, Aida M, Honjo T. An evolutionary view of the mechanism for immune and genome diversity. THE JOURNAL OF IMMUNOLOGY 2012; 188:3559-66. [PMID: 22492685 DOI: 10.4049/jimmunol.1102397] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An ortholog of activation-induced cytidine deaminase (AID) was, evolutionarily, the first enzyme to generate acquired immune diversity by catalyzing gene conversion and probably somatic hypermutation (SHM). AID began to mediate class switch recombination (CSR) only after the evolution of frogs. Recent studies revealed that the mechanisms for generating immune and genetic diversity share several critical features. Meiotic recombination, V(D)J recombination, CSR, and SHM all require H3K4 trimethyl histone modification to specify the target DNA. Genetic instability related to dinucleotide or triplet repeats depends on DNA cleavage by topoisomerase 1, which also initiates DNA cleavage in both SHM and CSR. These similarities suggest that AID hijacked the basic mechanism for genome instability when AID evolved in jawless fish. Thus, the risk of introducing genome instability into nonimmunoglobulin loci is unavoidable but tolerable compared with the advantage conferred on the host of being protected against pathogens by the enormous Ig diversification.
Collapse
Affiliation(s)
- Lucia Kato
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | | | | | | | | | | |
Collapse
|
34
|
Begum NA, Honjo T. Evolutionary comparison of the mechanism of DNA cleavage with respect to immune diversity and genomic instability. Biochemistry 2012; 51:5243-56. [PMID: 22712724 DOI: 10.1021/bi3005895] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is generally assumed that the genetic mechanism for immune diversity is unique and distinct from that for general genome diversity, in part because of the high efficiency and strict regulation of immune diversity. This expectation was partially met by the discovery of RAG1 and -2, which catalyze V(D)J recombination to generate the immune repertoire of B and T lymphocyte receptors. RAG1 and -2 were later shown to be derived from a transposon. On the other hand, activation-induced cytidine deaminase (AID), which mediates both somatic hypermutation (SHM) and the class-switch recombination (CSR) of the immunoglobulin genes, evolved earlier than RAG1 and -2 in jawless vertebrates. This review compares immune diversity and general genome diversity from an evolutionary perspective, shedding light on the roles of DNA-cleaving enzymes and target recognition markers. This comparison revealed that AID-mediated SHM and CSR share the cleaving enzyme topoisomerase 1 with transcription-associated mutation (TAM) and triplet contraction, which is involved in many genetic diseases. These genome-altering events appear to target DNA with non-B structure, which is induced by the inefficient correction of the excessive supercoiling that is caused by active transcription. Furthermore, an epigenetic modification on chromatin (histone H3K4 trimethylation) is used as a mark for DNA cleavage sites in meiotic recombination, V(D)J recombination, CSR, and SHM. We conclude that acquired immune diversity evolved via the appearance of an AID orthologue that utilized a preexisting mechanism for genomic instability, such as TAM.
Collapse
Affiliation(s)
- Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | | |
Collapse
|
35
|
Häsler J, Rada C, Neuberger MS. The cytoplasmic AID complex. Semin Immunol 2012; 24:273-80. [PMID: 22698843 DOI: 10.1016/j.smim.2012.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/18/2012] [Indexed: 12/28/2022]
Abstract
Although AID fulfils its physiological function of diversifying antibody genes in the nucleus, most of the AID protein within the cell is found in a complex located in the cytoplasm. In this review, we summarize what is currently known about this cytoplasmic AID complex. Its size has been estimated to lie between 300 and 500kDa (sedimentation coefficient of 10-11S) and it comprises the abundant protein translation elongation factor 1α (eEF1A) as a major stoichiometric component. We speculate on the possible roles of this complex as well as of chaperones known to interact with AID in regulating the cytosolic retention of AID and its controlled release for import into the nucleus.
Collapse
Affiliation(s)
- Julien Häsler
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
| | | | | |
Collapse
|
36
|
Renshaw SA, Trede NS. A model 450 million years in the making: zebrafish and vertebrate immunity. Dis Model Mech 2012; 5:38-47. [PMID: 22228790 PMCID: PMC3255542 DOI: 10.1242/dmm.007138] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Since its first splash 30 years ago, the use of the zebrafish model has been extended from a tool for genetic dissection of early vertebrate development to the functional interrogation of organogenesis and disease processes such as infection and cancer. In particular, there is recent and growing attention in the scientific community directed at the immune systems of zebrafish. This development is based on the ability to image cell movements and organogenesis in an entire vertebrate organism, complemented by increasing recognition that zebrafish and vertebrate immunity have many aspects in common. Here, we review zebrafish immunity with a particular focus on recent studies that exploit the unique genetic and in vivo imaging advantages available for this organism. These unique advantages are driving forward our study of vertebrate immunity in general, with important consequences for the understanding of mammalian immune function and its role in disease pathogenesis.
Collapse
Affiliation(s)
- Stephen A Renshaw
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | | |
Collapse
|
37
|
Zhu C, Lee V, Finn A, Senger K, Zarrin AA, Du Pasquier L, Hsu E. Origin of immunoglobulin isotype switching. Curr Biol 2012; 22:872-80. [PMID: 22542103 DOI: 10.1016/j.cub.2012.03.060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/02/2012] [Accepted: 03/19/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND From humans to frogs, immunoglobulin class switching introduces different effector functions to antibodies through an intrachromosomal DNA recombination process at the heavy-chain locus. Although there are two conventional antibody classes (IgM, IgW) in sharks, their heavy chains are encoded by 20 to >100 miniloci. These representatives of the earliest jawed vertebrates possess a primordial immunoglobulin gene organization where each gene cluster is autonomous and contains a few rearranging gene segments (VH-D1-D2-JH) with one constant region, μ or ω. RESULTS V(D)J rearrangement always takes place within the μ cluster, but here we show that the VDJ can be expressed with constant regions from different clusters, although IgH genes are spatially distant, at >120 kb. Moreover, reciprocal exchanges take place between Igω and Igμ genes. Switching is augmented with deliberate immunization and is concomitant with somatic hypermutation activity. Because switching occurs independently of the partners' linkage position, some events involve transchromosomal recombination. The switch sites consist of direct joins between two genes in the 3' intron flanking JH. CONCLUSIONS Our data are consistent with a mechanism of cutting or joining of distal DNA lesions initiated by activation-induced cytidine deaminase (AID), in the absence of mammalian-type switch regions. We suggest that, in shark, with its many autonomous IgH targeted by programmed DNA breakage, factors predisposing broken DNA ends to translocate configured the earliest version of class switch recombination.
Collapse
Affiliation(s)
- Catherine Zhu
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Lackey L, Demorest ZL, Land AM, Hultquist JF, Brown WL, Harris RS. APOBEC3B and AID have similar nuclear import mechanisms. J Mol Biol 2012; 419:301-14. [PMID: 22446380 DOI: 10.1016/j.jmb.2012.03.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 11/17/2022]
Abstract
Members of the APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) protein family catalyze DNA cytosine deamination and underpin a variety of immune defenses. For instance, several family members, including APOBEC3B (A3B), elicit strong retrotransposon and retrovirus restriction activities. However, unlike the other proteins, A3B is the only family member with steady-state nuclear localization. Here, we show that A3B nuclear import is an active process requiring at least one amino acid (Val54) within an N-terminal motif analogous to the nuclear localization determinant of the antibody gene diversification enzyme AID (activation-induced cytosine deaminase). Mechanistic conservation with AID is further suggested by A3B's capacity to interact with the same subset of importin proteins. Despite these mechanistic similarities, enforced A3B expression cannot substitute for AID-dependent antibody gene diversification by class switch recombination. Regulatory differences between A3B and AID are also visible during cell cycle progression. Our studies suggest that the present-day A3B enzyme retained the nuclear import mechanism of an ancestral AID protein during the expansion of the APOBEC3 locus in primates. Our studies also highlight the likelihood that, after nuclear import, specialized mechanisms exist to guide these enzymes to their respective physiological substrates and prevent gratuitous chromosomal DNA damage.
Collapse
Affiliation(s)
- Lela Lackey
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | |
Collapse
|
39
|
Dancyger AM, King JJ, Quinlan MJ, Fifield H, Tucker S, Saunders HL, Berru M, Magor BG, Martin A, Larijani M. Differences in the enzymatic efficiency of human and bony fish AID are mediated by a single residue in the C terminus modulating single‐stranded DNA binding. FASEB J 2011; 26:1517-25. [DOI: 10.1096/fj.11-198135] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alex M. Dancyger
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| | - Justin J. King
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| | - Matthew J. Quinlan
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| | - Heather Fifield
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| | - Stephanie Tucker
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| | - Holly L. Saunders
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Maribel Berru
- Department of ImmunologyUniversity of TorontoTorontoOntarioCanada
| | - Bradley G. Magor
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Alberto Martin
- Department of ImmunologyUniversity of TorontoTorontoOntarioCanada
| | - Mani Larijani
- Program in Immunology and Infectious DiseasesDivision of Biomedical SciencesFaculty of MedicineMemorial University of NewfoundlandSt. John'sNewfoundlandCanada
| |
Collapse
|
40
|
Barreto VM, Magor BG. Activation-induced cytidine deaminase structure and functions: a species comparative view. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:991-1007. [PMID: 21349283 DOI: 10.1016/j.dci.2011.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 02/09/2011] [Accepted: 02/16/2011] [Indexed: 05/30/2023]
Abstract
In the ten years since the discovery of activation-induced cytidine deaminase (AID) there has been considerable effort to understand the mechanisms behind this enzyme's ability to target and modify immunoglobulin genes leading to somatic hypermutation and class switch recombination. While the majority of research has focused on mouse and human models of AID function, work on other species, from lamprey to rabbit and sheep, has taught us much about the scope of functions of the AID mutator. This review takes a species-comparative approach to what has been learned about the AID mutator enzyme and its role in humoral immunity.
Collapse
|
41
|
Chen K, Cerutti A. The function and regulation of immunoglobulin D. Curr Opin Immunol 2011; 23:345-52. [PMID: 21353515 DOI: 10.1016/j.coi.2011.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 01/25/2011] [Accepted: 01/27/2011] [Indexed: 12/22/2022]
Abstract
Recent discoveries of IgD in ancient vertebrates suggest that IgD has been preserved in evolution from fish to human for important immunological functions. A non-canonical form of class switching from IgM to IgD occurs in the human upper respiratory mucosa to generate IgD-secreting B cells that bind respiratory bacteria and their products. In addition to enhancing mucosal immunity, IgD class-switched B cells enter the circulation to 'arm' basophils and other innate immune cells with secreted IgD. Although the nature of the IgD receptor remains elusive, cross-linking of IgD on basophils stimulates release of immunoactivating, proinflammatory and antimicrobial mediators. This pathway is dysregulated in autoinflammatory disorders such as hyper-IgD syndrome, indicating that IgD orchestrates an ancestral surveillance system at the interface between immunity and inflammation.
Collapse
Affiliation(s)
- Kang Chen
- Immunology Institute, Department of Medicine, Mount Sinai School of Medicine, One Gustave, L. Levy Place, New York, NY 10029, USA
| | | |
Collapse
|
42
|
Das S, Hirano M, McCallister C, Tako R, Nikolaidis N. Comparative genomics and evolution of immunoglobulin-encoding loci in tetrapods. Adv Immunol 2011; 111:143-78. [PMID: 21970954 DOI: 10.1016/b978-0-12-385991-4.00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The immunoglobulins (Igs or antibodies) as an integral part of the tetrapod adaptive immune response system have evolved toward producing highly diversified molecules that recognize a remarkably large number of different antigens. Antibodies and their respective encoding loci have been shaped by different and often contrasting evolutionary forces, some of which aim to conserve an established pattern or mechanism and others to generate alternative and diversified structural and functional configurations. The genomic organization, gene content, ratio between functional genes and pseudogenes, number and position of recombining genetic elements, and the different levels of divergence present at the germline of the Ig-encoding loci have been evolutionarily shaped and optimized in a lineage- and, in some cases, species-specific mode aiming to increase organismal fitness. Further, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, such as V(D)J recombination, class switch recombination, isotype exclusion, somatic hypermutation, and gene conversion. Diverse tetrapod species, based on their specific germline configurations, use these mechanisms in several different combinations to effectively generate a vast array of distinct antibody types and structures. This chapter summarizes our current knowledge on the Ig-encoding loci in tetrapods and discusses the different evolutionary mechanisms that shaped their diversification.
Collapse
Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, Georgia, USA
| | | | | | | | | |
Collapse
|
43
|
Pinaud E, Marquet M, Fiancette R, Péron S, Vincent-Fabert C, Denizot Y, Cogné M. The IgH locus 3' regulatory region: pulling the strings from behind. Adv Immunol 2011; 110:27-70. [PMID: 21762815 DOI: 10.1016/b978-0-12-387663-8.00002-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antigen receptor gene loci are among the most complex in mammals. The IgH locus, encoding the immunoglobulin heavy chain (IgH) in B-lineage cells, undergoes major transcription-dependent DNA remodeling events, namely V(D)J recombination, Ig class-switch recombination (CSR), and somatic hypermutation (SHM). Various cis-regulatory elements (encompassing promoters, enhancers, and chromatin insulators) recruit multiple nuclear factors in order to ensure IgH locus regulation by tightly orchestrated physical and/or functional interactions. Among major IgH cis-acting regions, the large 3' regulatory region (3'RR) located at the 3' boundary of the locus includes several enhancers and harbors an intriguing quasi-palindromic structure. In this review, we report progress insights made over the past decade in order to describe in more details the structure and functions of IgH 3'RRs in mouse and human. Generation of multiple cellular, transgenic and knock-out models helped out to decipher the function of the IgH 3' regulatory elements in the context of normal and pathologic B cells. Beside its interest in physiology, the challenge of elucidating the locus-wide cross talk between distant cis-regulatory elements might provide useful insights into the mechanisms that mediate oncogene deregulation after chromosomal translocations onto the IgH locus.
Collapse
Affiliation(s)
- Eric Pinaud
- UMR CNRS 6101, Centre National de la Recherche Scientifique, Université de Limoges, Limoges, France
| | | | | | | | | | | | | |
Collapse
|
44
|
Marianes AE, Zimmerman AM. Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish. Immunology 2010; 132:240-55. [PMID: 21070232 DOI: 10.1111/j.1365-2567.2010.03358.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In mammals, somatic hypermutation (SHM) of immunoglobulin (Ig) genes is critical for the generation of high-affinity antibodies and effective immune responses. Knowledge of sequence-specific biases in the targeting of somatic mutations can be useful for studies aimed at understanding antibody repertoires produced in response to infections, B-cell neoplasms, or autoimmune disease. To evaluate potential nucleotide targets of somatic mutation in zebrafish (Danio rerio), an enriched IgL cDNA library was constructed and > 250 randomly selected clones were sequenced and analysed. In total, 55 unique VJ-C sequences were identified encoding a total of 125 mutations. Mutations were most prevalent in V(L) with a bias towards single base transitions and increased mutation in the complementarity-determining regions (CDRs). Overall, mutations were overrepresented at WRCH/DGYW motifs suggestive of activation-induced cytidine deaminase (AID) targeting which is common in mice and humans. In contrast to mammalian models, N and P addition was not observed and mutations at AID hotspots were largely restricted to palindromic WRCH/DGYW motifs. Mutability indexes for di- and trinucleotide combinations confirmed C/G targets within WRCH/DGYW motifs to be statistically significant mutational hotspots and showed trinucleotides ATC and ATG to be mutation coldspots. Additive mutations in VJ-C sequences revealed patterns of clonal expansion consistent with affinity maturation responses seen in higher vertebrates. Taken together, the data reveal specific nucleotide targets of SHM in zebrafish and suggest that AID and affinity maturation contribute to antibody diversification in this emerging immunological model.
Collapse
Affiliation(s)
- Alexis E Marianes
- Department of Biology, College of Charleston, Charleston, SC 29424, USA
| | | |
Collapse
|
45
|
Edholm ES, Bengtén E, Stafford JL, Sahoo M, Taylor EB, Miller NW, Wilson M. Identification of two IgD+ B cell populations in channel catfish, Ictalurus punctatus. THE JOURNAL OF IMMUNOLOGY 2010; 185:4082-94. [PMID: 20817869 DOI: 10.4049/jimmunol.1000631] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Channel catfish Ictalurus punctatus express two Ig isotypes: IgM and IgD. Although catfish IgM has been extensively studied at the functional and structural levels, much less is known about IgD. In this study, IgM(+)/IgD(+) and IgM(-)/IgD(+) catfish B cell populations were identified through the use of anti-IgM and anti-IgD mAbs. Catfish IgM(+)/IgD(+) B cells are small and agranular. In contrast, IgM(-)/IgD(+) B cells are larger and exhibit a plasmablast morphology. The use of cell sorting, flow cytometry, and RT-PCR demonstrated that IgD(+) B cell expression varies among individuals. For example, some catfish have <5% IgM(-)/IgD(+) B cells in their PBLs, whereas in others the IgM(-)/IgD(+) B cell population can represent as much as 72%. Furthermore, IgD expressed by IgM(-)/IgD(+) B cells preferentially associates with IgL σ. Comparatively, IgM(+)/IgD(+) B cells can express any of the four catfish IgL isotypes. Also, transfection studies show that IgD functions as a typical BCR, because Igδ-chains associate with CD79a and CD79b molecules, and all membrane IgD transcripts from sorted IgM(-)/IgD(+) B cells contain viable VDJ rearrangements, with no bias in family member usage. Interestingly, all secreted IgD transcripts from IgM(+)/IgD(+) and IgM(-)/IgD(+) B cells were V-less and began with a leader spliced to Cδ1. Importantly, transfection of catfish clonal B cells demonstrated that this leader mediated IgD secretion. Together, these findings imply that catfish IgM(-)/IgD(+) B cells likely expand in response to certain pathogens and that the catfish IgD Fc-region, as has been suggested for human IgD, may function as a pattern recognition molecule.
Collapse
Affiliation(s)
- Eva-Stina Edholm
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Saunders HL, Oko AL, Scott AN, Fan CW, Magor BG. The cellular context of AID expressing cells in fish lymphoid tissues. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:669-676. [PMID: 20105439 DOI: 10.1016/j.dci.2010.01.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 01/18/2010] [Accepted: 01/20/2010] [Indexed: 05/28/2023]
Abstract
It has long been held that the cold-blooded vertebrates lack mammalian-like germinal centers, though they do have affinity maturation and the immunoglobulin mutator activation-induced cytidine deaminase or AID. Using AID as a marker of sites of somatic hypermutation, we have identified discrete cell clusters of up to several thousand cells, in the spleen and kidney of channel catfish (Ictalurus punctatus), which may be primordial germinal centers. In situ hybridization revealed that AID expressing cells are interspersed or surrounded by a population of pigmented CSF1-R expressing cells called melano-macrophages. Significantly, melano-macrophages or associated reticular cells have been previously noted for their ability to retain soluble antigen on or near their surface for several weeks following vaccination. Laser capture microdissection and RT-PCR were used to establish that these cell clusters also contained cells expressing Ig heavy chain transcripts as well as transcripts of TcRbeta and the putative CD4 homologue of fish. These observations, coupled with past work showing that mutations develop in B-cell lineages in fishes, allow us to develop a model for how affinity maturation may have evolved in early gnathostome vertebrates.
Collapse
Affiliation(s)
- Holly L Saunders
- Department of Biological Sciences, University of Alberta, Edmonton, T6G-2E5 Canada
| | | | | | | | | |
Collapse
|
47
|
Misaghi S, Garris CS, Sun Y, Nguyen A, Zhang J, Sebrell A, Senger K, Yan D, Lorenzo MN, Heldens S, Lee WP, Xu M, Wu J, DeForge L, Sai T, Dixit VM, Zarrin AA. Increased targeting of donor switch region and IgE in Sgamma1-deficient B cells. THE JOURNAL OF IMMUNOLOGY 2010; 185:166-73. [PMID: 20511552 DOI: 10.4049/jimmunol.1000515] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ab class switch recombination involves a recombination between two repetitive DNA sequences known as switch (S) regions that vary in length, content, and density of the repeats. Abs expressed by B cells are diversified by somatic hypermutation and class switch recombination. Both class switch recombination and somatic hypermutation are initiated by activation-induced cytidine deaminase (AID), which preferentially recognizes certain hot spots that are far more enriched in the S regions. We found that removal of the largest S region, Sgamma1 (10 kb), in mice can result in the accumulation of mutations and short-range intra-S recombination in the donor Smu region. Furthermore, elevated levels of IgE were detected in trinitrophenol-OVA-immunized mice and in anti-CD40 plus IL-4-stimulated B cells in vitro. We propose that AID availability and targeting in part might be regulated by its DNA substrate. Thus, prominently transcribed S regions, such as Sgamma1, might provide a sufficient sink for AID protein to titrate away AID from other accessible sites within or outside the Ig locus.
Collapse
Affiliation(s)
- Shahram Misaghi
- Department of Physiological Chemistry, Genentech, San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Fagarasan S, Kawamoto S, Kanagawa O, Suzuki K. Adaptive immune regulation in the gut: T cell-dependent and T cell-independent IgA synthesis. Annu Rev Immunol 2010; 28:243-73. [PMID: 20192805 DOI: 10.1146/annurev-immunol-030409-101314] [Citation(s) in RCA: 358] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In mammals, the gastrointestinal tract harbors an extraordinarily dense and complex community of microorganisms. The gut microbiota provide strong selective pressure to the host to evolve adaptive immune responses required for the maintenance of local and systemic homeostasis. The continuous antigenic presence in the gut imposes a dynamic remodeling of gut-associated lymphoid tissues (GALT) and the selection of multiple layered strategies for immunoglobulin (Ig) A production. The composite and dynamic gut environment also necessitates heterogeneous, versatile, and convertible T cells, capable of inhibiting (Foxp3(+) T cells) or helping (T(FH) cells) local immune responses. In this review, we describe recent advances in our understanding of dynamic pathways that lead to IgA synthesis, in gut follicular structures and in extrafollicular sites, by T cell-dependent and T cell-independent mechanisms. We discuss the finely tuned regulatory mechanisms for IgA production and emphasize the role of mucosal IgA in the selection and maintenance of the appropriate microbial composition that is necessary for immune homeostasis.
Collapse
|
49
|
Regulation of activation-induced cytidine deaminase DNA deamination activity in B-cells by Ser38 phosphorylation. Biochem Soc Trans 2009; 37:561-8. [PMID: 19442251 DOI: 10.1042/bst0370561] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human and mouse Ig genes are diversified in mature B-cells by distinct processes known as Ig heavy-chain CSR (class switch recombination) and Ig variable-region exon SHM (somatic hypermutation). These DNA-modification processes are initiated by AID (activation-induced cytidine deaminase), a DNA cytidine deaminase predominantly expressed in activated B-cells. AID is post-transcriptionally regulated via multiple mechanisms, including microRNA regulation, nucleocytoplasmic shuttling, ubiquitination and phosphorylation. Among these regulatory processes, AID phosphorylation at Ser(38) has been a focus of particularly intense study and debate. In the present paper, we discuss recent biochemical and mouse genetic studies that begin to elucidate the functional significance of AID Ser(38) phosphorylation in the context of the evolution of this mode of AID regulation and the potential roles that it may play in activated B-cells during a normal immune response.
Collapse
|
50
|
Basu U, Franklin A, Alt FW. Post-translational regulation of activation-induced cytidine deaminase. Philos Trans R Soc Lond B Biol Sci 2009; 364:667-73. [PMID: 19010772 DOI: 10.1098/rstb.2008.0194] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The assembled immunoglobulin genes in the B cells of mice and humans are altered by distinct processes known as class switch recombination (CSR) and somatic hypermutation, leading to diversification of the antibody repertoire. These two DNA modification processes are initiated by the B cell-specific protein factor activation-induced cytidine deaminase (AID). AID is post-translationally modified by phosphorylation at multiple sites, although functional significance during CSR has been implicated only for phosphorylation at serine-38 (S38). Although multiple laboratories have demonstrated that AID function is regulated via phosphorylation at S38, the precise biological role of S38 phosphorylation has been a topic of debate. Here, we discuss our interpretation of the significance of AID regulation via phosphorylation and also discuss how this form of AID regulation may have evolved in higher organisms.
Collapse
Affiliation(s)
- Uttiya Basu
- Howard Hughes Medical Institute, The Children's Hospital, Boston, MA 02115, USA
| | | | | |
Collapse
|